First commit

ec_plot

+#!/bin/sh
+
+if [ $# -lt 1 ] ; then 
+  echo "Usage: `basename $0` <eddy current ecclog file>"
+  exit 0;
+fi
+
+logfile=$1;
+basenm=`basename $logfile .ecclog`;
+
+nums=`grep -n 'Final' $logfile | sed 's/:.*//'`; 
+
+touch grot_ts.txt
+touch grot.mat
+
+firsttime=yes;
+m=1;
+for n in $nums ; do 
+    echo "Timepoint $m"
+    n1=`echo $n + 1 | bc` ; 
+    n2=`echo $n + 5 | bc` ;
+    sed -n  "$n1,${n2}p" $logfile > grot.mat ; 
+    if [ $firsttime = yes ] ; then firsttime=no; cp grot.mat grot.refmat ; cp grot.mat grot.oldmat ; fi
+    absval=`$FSLDIR/bin/rmsdiff grot.mat grot.refmat $basenm`;
+    relval=`$FSLDIR/bin/rmsdiff grot.mat grot.oldmat $basenm`;
+    cp grot.mat grot.oldmat
+    echo $absval $relval >> ec_disp.txt ;
+    $FSLDIR/bin/avscale --allparams grot.mat $basenm | grep 'Rotation Angles' | sed 's/.* = //' >> ec_rot.txt ;
+    $FSLDIR/bin/avscale --allparams grot.mat $basenm | grep 'Translations' | sed 's/.* = //' >> ec_trans.txt ;
+    m=`echo $m + 1 | bc`;
+done
+
+echo "absolute" > grot_labels.txt
+echo "relative" >> grot_labels.txt
+
+$FSLDIR/bin/fsl_tsplot -i ec_disp.txt -t 'Eddy Current estimated mean displacement (mm)' -l grot_labels.txt -o ec_disp.png
+
+echo "x" > grot_labels.txt
+echo "y" >> grot_labels.txt
+echo "z" >> grot_labels.txt
+
+$FSLDIR/bin/fsl_tsplot -i ec_rot.txt -t 'Eddy Current estimated rotations (radians)' -l grot_labels.txt -o ec_rot.png
+$FSLDIR/bin/fsl_tsplot -i ec_trans.txt -t 'Eddy Current estimated translations (mm)' -l grot_labels.txt -o ec_trans.png
+
+# clean up temp files
+/bin/rm grot_labels.txt grot.oldmat grot.refmat grot.mat
+
+